The invention relates generally to automated systems and methods for extracting high-content information from whole organisms.
Organisms, such as teleosts, nematodes and fruit flies serve as biological models for a variety of research applications. For example, zebrafish is a well-known vertebrate model for developmental biology, molecular genetics, and toxicology studies. Zebrafish offer many advantages over other research models such as mice including the small size of zebrafish, low husbandry costs, ex utero transparent embryos, early morphology distinction, large number of embryos produced per mating, and the similarity of its genome to that of humans. Zebrafish are commonly used to study the effect of various drugs on cell apoptosis, organ development (e.g. brain, liver, tail, ear) as well as cardiac and nervous system functions.
Research using zebrafish as the model organism has extended to modeling human diseases and analyzing the formation and functions of cell populations in organs within the organism. This work has generated new human disease models and has begun to identify potential therapeutics, including genes that modify disease states and chemicals that rescue organs from disease.
The recent development of the zebrafish as a model for chemical genetics has established chemical screening in vivo as an adjunct to older screening technologies in cell lines or in vitro. Soluble chemicals permeate into zebrafish embryos and produce specific effects. In contrast to screening by in vitro techniques, zebrafish offers an in vivo vertebrate model for studying the bioactivity of chemicals. In addition, the availability of large numbers of zebrafish mutants makes chemical suppressor screens fast and straightforward. The targets of chemicals found to prevent or cure disease phenotypes in zebrafish will, in general, have very close cognates in humans. Therefore these screens promise to provide key entry points for the development of new therapeutic drugs.
In contrast to other vertebrate models, zebrafish complete embryogenesis in the first 72 hours post fertilization. Most of the internal organs, including the cardiovascular system, gut, liver and kidney, develop rapidly in the first 24 to 48 hour. Zebrafish embryos are also transparent, which facilitates observation and analysis. All the precursor tissues of the brain, eyes, heart and musculature can be easily visualized using light microscopy. Another important advantage of this animal model is that the morphological and molecular basis of tissue and organ development is, in general, either identical or similar to other vertebrates, including humans. Use of zebrafish as an alternative animal model for mammals accelerates research and is less expensive than large animal testing.
However, use of zebrafish for preclinical testing requires the researcher to take various anatomical measurements such as, but not limited to, liver size, tail length and curvature, size and frequency of spots, and the presence or absence of axons. At present, these measurements are typically obtained manually, or using generic imaging software and manual tracing of image features. Such methods are time consuming and inefficient given the small size of these research models and subject to human bias. One approach is to develop image analysis algorithms specific to the observable phenotypes of each assay. While the latter method can be functional, it is inefficient in that time and effort must be spent for each specific assay.
Although various methods exist that use atlases of various anatomical features to guide such generic segmentation and registration software, such methods are deficient or otherwise not capable of registering the atlases on an actual organism without substantial augmentation. Although methods exist that are capable of imaging small portions of a nematode research model at the cellular level, these methods are not capable of automatically imaging and mapping whole research models. These methods are also not adapted for use in automated screening.
Currently, automated, medium- or high-throughput systems and methods do not exist for quantitatively measuring and analyzing whole, but small, organisms, such as zebrafish, which are necessary to make them a viable alternative to larger research models such as mice.